def test_dijkstra_vs_networkx_apsp(): """ Test Dijkstra: My implementation vs Networkx implementation > All Pairs """ # NX Version G = nx.from_edgelist(edgelist_james) nx.set_edge_attributes(G, 'weight', edgelist_james) nx_all_complete_paths = nx.all_pairs_dijkstra_path(G, 'weight') # My Version d = Dijkstra() d.from_edgelist(edgelist_james, directed=False) dc_all_lenghts, dc_all_paths = d.all_pairs_shortest_paths() dc_all_complete_paths = d.shortest_complete_paths assert (nx_all_complete_paths == dc_all_complete_paths)
def test_dijkstra_vs_networkx_single_source_all_lenghts_and_paths():
""" Test Dijkstra: Rion's implementation vs Networkx implementation > Single Source """
# NX Version
G = nx.from_edgelist(edgelist_james)
nx.set_edge_attributes(G, 'weight', edgelist_james)
nx_lenghts = nx.single_source_dijkstra_path_length(G, source='s', weight='weight')
nx_paths = nx.single_source_dijkstra_path(G, source='s', weight='weight')
# My Version
d = Dijkstra()
d.from_edgelist(edgelist_james, directed=False)
dc_lenghts, dc_paths = d.single_source_shortest_paths('s', kind='metric')
assert (nx_lenghts == dc_lenghts)
assert (nx_paths == dc_paths)
def compute_metric_backbone(G):
print('> Computing Dijkstra APSP')
dict_edges = {(i, j): prox2dist(d['weight'])
for i, j, d in G.edges(data=True)}
dij = Dijkstra.from_edgelist(dict_edges, directed=False, verbose=10)
print('> Metric')
poolresults = list(range(len(dij.N)))
for node in dij.N:
print('> Dijkstra node {node:d} of {n_nodes:d}'.format(node=node + 1,
n_nodes=len(
dij.N)))
poolresults[node] = _cy_single_source_shortest_distances(
node, dij.N, dij.E, dij.neighbors, ('min', 'sum'), verbose=2)
shortest_distances, local_paths = map(list, zip(*poolresults))
dij.shortest_distances = dict(zip(dij.N, shortest_distances))
MSD = dij.get_shortest_distances(format='dict', translate=True)
#
dict_edges_backbone = {}
dict_edges_s_values = {}
for (i, j), d in dict_edges.items():
# Backbone = distance == distance-closure
if d == MSD[i][j]:
dict_edges_backbone[(i, j)] = True
else:
dict_edges_backbone[(i, j)] = False
# S-Value = distance / distance-closure
dict_edges_s_values[(i, j)] = d / MSD[i][j]
return dict_edges_backbone, dict_edges_s_values
def test_dijkstra_sssp_from_edgelist(): """ Test Dijkstra: Single Source Shortest Path (SSSP) from Edgelist """ dij = Dijkstra(verbose=True) dij.from_edgelist(edgelist_james) dij.single_source_shortest_paths(source='s', kind='metric')
def test_dijkstra_sssp_from_numpy(): """ Test Dijkstra: Single Source Shortest Path (SSSP) from Numpy """ dij = Dijkstra(verbose=True) dij.from_numpy_matrix(D) dij.single_source_shortest_paths(source=0, kind='metric')
# Build Networkx object
print('--- Building Network ---')
# C for Correlation network
G = nx.from_pandas_adjacency(df, create_using=nx.Graph)
# P for Proximity network (which in this case is a Correlation)
P = [w for i, j, w in G.edges.data('weight')]
# Converts (P)roximity to (D)istance using a map.
D_dict = dict(zip(G.edges(), map(prox2dist, P)))
# Set the distance value for each edge
nx.set_edge_attributes(G, name='distance', values=D_dict)
# Compute closure (Using the Dijkstra Class directly)
print('--- Computing Dijkstra APSP ---')
dij = Dijkstra.from_edgelist(D_dict, directed=False, verbose=10)
# Serial Computation
poolresults = list(range(len(dij.N)))
for node in dij.N:
print('> Dijkstra node %s of %s' % (node + 1, len(dij.N)))
# Computes the shortest distance and paths between a source node and every other node
poolresults[node] = _cy_single_source_shortest_distances(
node, dij.N, dij.E, dij.neighbours, ('min', 'sum'), verbose=10)
shortest_distances, local_paths = map(list, zip(*poolresults))
dij.shortest_distances = dict(zip(dij.N, shortest_distances))
# (S)hortest (D)istances
SD = dij.get_shortest_distances(format='dict', translate=True)
print('> Done.')
print('> Populating (G)raph')
# Mapping results to triplet (i, j): v - Convert Dict-of-Dicts to Dict